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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from os import symlink
from spack import *
class Homer(Package):
"""Software for motif discovery and next generation sequencing analysis"""
homepage = "http://homer.ucsd.edu/homer"
url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.1.zip"
version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9')
depends_on('perl', type=('build', 'run'))
depends_on('r-biocgenerics', type='run')
depends_on('r-biocparallel', type='run')
depends_on('r-edger', type='run')
depends_on('r-deseq2', type='run')
variant('data', default=False,
description='Download genome data packages')
def install(self, spec, prefix):
# initialize homer directories
basedir = join_path(prefix.lib, 'homer')
mkdirp(basedir)
install_tree('.', basedir)
# symlink bin so it is included in the PATH
symlink(join_path(basedir, 'bin'), prefix.bin)
# override homer base directory in configure script
filter_file('my $homeDir = $1;',
'my $homeDir = \"{0}\";'.format(basedir),
'configureHomer.pl', string=True)
# compile/prepare binaries and perl scripts with the correct paths
perl = which('perl')
perl('configureHomer.pl', '-local')
# download extra data if requested
if '+data' in spec:
perl('configureHomer.pl', '-install', '-all')
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